class: top, left, inverse, title-slide # Untangling biodiversity changes<br>across a continuum of spatial scales ## <br><br>PhD Presentation ### <br><br>PhD candidate: François Leroy<br>Supervisor: Petr Keil ### Czech University of Life Sciences<br>Prague --- # Biodiversity changes are scale dependent * **Global** biodiversity is **declining** -- * **Local, regional or national** trends are **not always** similar <img src="data:image/png;base64,#images/litrev.jpg" width="2604" height="430px" /> --- # Biodiversity changes are scale dependent * **Global** biodiversity is **declining** * **Local, regional or national** trends are **not always** similar <br><br><br><br> .center[ ### `\(\Rightarrow\)` Dynamic processes (*i.e.* colonization, extinction, turnover...) vary with spatial scales ] --- class: inverse, center, middle ## Biodiversity trends have to be assessed across spatial (and temporal) scales --- # Scales * **Spatial grain** <br><br><br> .center[ <img src="data:image/png;base64,#images/spatialgrain.jpg" width="1831" /> ] --- # Scales * **Temporal grain** <br><br><br> .center[ <img src="data:image/png;base64,#images/temporalgrain.jpg" width="80%" /> ] --- # Biodiversity data * One dataset express the biodiversity at its specific spatial and temporal grains * Data heterogeneity in spatial and temporal grains and extent * Lack of data -- <br><br> ## Problem: With the actual data, it is not straight forward to assess biodiversity trends for a continuum of spatial scales --- # Spatial aggregation **Jarzyna *et al* (2015)** <img align="right" src="data:image/png;base64,#images/jarzyna2015.jpg" width="75%"/> <br><br><br><br><br><br><br> **Chase *et al.* (2019)** .center[ <img src="data:image/png;base64,#images/chase_2019.PNG" width="40%" /> ] --- # Model .pull-left[ * Use biodiversity data with heterogeneous: **spatial grain, temporal grain, location, spatial extent and temporal extent**. <br><br> * Use this component as **covariates** to predict species richness at desired (spatial & temporal) grain and location (in space & time) ] .pull-right[ <img src="data:image/png;base64,#images/keil_chase_title.PNG" width="1529" /> .center[ <img src="data:image/png;base64,#images/keil_chase_2022.PNG" width="75%" /> ] ] --- # Model <br><br> **In practice:** ``` treeBasedModel(species richness ~ area, -> Species-area relationship temporal grain, -> Species-time relationship latitude, -> Location in space longitude, -> Location in space date) -> Location in time ``` <br> Tree based models: the flexibility grasps the interactions between **species area/time relationship** and their location in space and time. -- <br><br> .center[ ### `\(\Rightarrow\)` We need data at different spatial and temporal grains ] --- # Atlas dataset .pull-left[ .center[**Temporal scales**] 3 time periods, 3 different time spans: * M2 = 1985-1989 (**5 years**) * M3 = 2001-2003 (**3 years**) * M4 = 2014-2017 (**4 years**) ] .pull-right[ .center[**Spatial scales**] Large scale dataset. Ranging from less than **100 Km** `\(^2\)` to **80 000 Km** `\(^2\)` (the entire Czech Republic) <img src="data:image/png;base64,#images/spatialgrain_atlas.jpg" width="1608" /> ] -- <br><br> .center[ ### `\(\Rightarrow\)` The model homogenize the temporal grain and the sampling effort ] --- # Breeding bird survey (BBS) dataset <div id="htmlwidget-dc75008b7bdced9988f7" style="width:100%;height:504px;" class="leaflet html-widget"></div> <script type="application/json" data-for="htmlwidget-dc75008b7bdced9988f7">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"setView":[[50,15.5],7.49,[]],"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,"OSM",{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a 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area"],{"collapsed":false,"autoZIndex":true,"position":"topright"}]},{"method":"addLayersControl","args":[[],["Points","Transect area"],{"collapsed":false,"autoZIndex":true,"position":"topright"}]},{"method":"hideGroup","args":["Transect area"]}],"limits":{"lat":[48.6241242955623,50.95805],"lng":[12.3057602889857,18.6290362411083]}},"evals":[],"jsHooks":[]}</script> ] --- # Performance .pull-left[ **Atlas model** `\(XGBoost\)` `\(R^2 = 0.77\)` `\(MAE = 9\)` <!-- ``` --> <!-- species richness ~ area, --> <!-- temporal grain, --> <!-- latitude, --> <!-- longitude, --> <!-- date, --> <!-- sampling effort, --> <!-- shape, --> <!-- elevation) --> <!-- ``` --> <img src="data:image/png;base64,#images/obsvspred_atlas.JPG" width="90%" /> ] .pull-right[ **BBS model** `\(Random Forest\)` `\(R^2 = 0.74\)` `\(MAE = 10\)` <img src="data:image/png;base64,#images/obsvspred_bbs.JPG" width="90%" /> ] --- # Richness change across scales * For each spatial scale: predictions of species richness from 1987 to 2017 * Assessment of the species richness change per year <br><br> <img src="data:image/png;base64,#images/spatialgrain.jpg" width="1831" /> --- # Richness change across scales .center[ <img src="data:image/png;base64,#images/srtrend.jpg" width="85%" /> ] --- # Richness change across scales .center[ <img src="data:image/png;base64,#images/srtrend_details.jpg" width="1369" /> ] --- # Species richness and spatial scale : the SAR .pull-left[ <br><br> - **SAR** = Species Area Relationship (Arrhenius 1921) <br><br><br> - Linear on a log-log scale <!-- <br> --> <!-- - The slope indicates the spatial `\(\beta-diversity\)` --> <!-- <br> --> <!-- - Can be used to extrapolate species richness (*e.g.* Kunin *et al.* 2018) --> ] .pull-right[ <img src="data:image/png;base64,#images/sar.png" width="800" height="430px" /> .credit[Brown *et al.* 2007] ] --- # Species richness and temporal scale: the STR .pull-left[ <br><br> - **STR** = Species-Time Relationship <br><br><br> - Can also be well described by a power law <!-- <br> --> <!-- - Emerges from both sampling and ecological processes --> <!-- <br> --> <!-- .center[**And... we don't know much more about it**] --> ] .pull-right[ <img src="data:image/png;base64,#images/str.png" width="552" height="430px" /> .credit[STR of the Breeding Bird Survey for different North American states, White 2004] ] --- # Species richness, space and time: the STAR .pull-left[ <br> - **STAR** = Species-Time-Area Relationship <!-- <br> --> <!-- - Results from both environmental variability and biological processes --> <br><br><br> <!-- The STAR raises the question: --> <!-- <br> --> .center[**Temporal and spatial scales highly drive species richness**] ] .pull-right[ <img src="data:image/png;base64,#images/star.png" width="352" /> .credit[Plant species richness as a function of interacting space and time, Adler & Lauenroth 2003] ] --- class: inverse, center, middle What about the relationship between space, time and... ## Species richness <span style="color: red;">trends</span> ? --- # Biodiversity changes and spatial scales <br><br> .pull-left[ * According to the taxa: .center[*"Species richness change can increase, decrease, reverse or be unimodal accross spatial scales."*] * For North American birds, larger spatial scales seem to increase positively the species richness (Oikos, Chase *et al* 2019) <br> ] .pull-right[ .center[ <img src="data:image/png;base64,#images/chase_2019.PNG" width="100%" /> ] ] --- # Biodiversity changes and temporal scales... <br><br><br> .center[...nothing in sight in the scientific literature] --- class: inverse, center, middle # Problematic: ### What are the links between <span style="color: red;">species-richness trends</span> and <span style="color: red;">spatio-temporal scales</span>? -- <br><br><br> <b>Taxon:</b> Birds <b>Location:</b> So far Czech Republic <b>Methods:</b> Machine learning (CART, GLM...) --- class: inverse, center, middle # Goal Use heterogeneous avian biodiversity datasets to model species richness trends across continuums of space and time scales .center[ <img src="data:image/png;base64,#images/star.png" width="352" /> ] --- # Datasets <br> We need heterogeneous datasets with: * Time series (for the trend) * Several spatial scales * Several temporal scales <br><br> 2 datasets: 1. The **atlas** data from the Czech Society for Ornithology (Česká společnost ornitologická). Courtesy of Vladimír Bejček, Karel Šťastný and Ivan Mikuláš. 2. Local time series from the **Breeding Bird Survey** (Jednotný program sčítání ptáků). Courtesy of Jiří Reif. --- <!-- # The Atlas dataset --> <!-- ```{r} --> <!-- ## Load the shps --> <!-- shps_names <- list.files("../phd/data/czech_bird/ATLASCR_DATA/Shapefile_Quadrats_CR/")[grepl("shp(?!.*xml)", list.files("../phd/data/czech_bird/ATLASCR_DATA/Shapefile_Quadrats_CR/"), perl = T)] --> <!-- shps_path <- --> <!-- list.files("../phd/data/czech_bird/ATLASCR_DATA/Shapefile_Quadrats_CR/", full.names = TRUE)[grepl("shp(?!.*xml)", list.files("../phd/data/czech_bird/ATLASCR_DATA/Shapefile_Quadrats_CR/"), perl = T)] --> <!-- for(i in 1:length(shps_names)){ --> <!-- assign(shps_names[i], --> <!-- st_read(shps_path[i], quiet = T) %>% st_transform(., crs = 4326)) --> <!-- } --> <!-- # Loading the countries shp: --> <!-- shp_country <- ne_countries(scale = "medium", returnclass = "sf") --> <!-- ``` --> <!-- .pull-left[ --> <!-- .center[**Temporal scales**] --> <!-- 4 time periods, 3 different time spans: --> <!-- * M1 = 1973-1977 (**5 years**) --> <!-- * M2 = 1985-1989 (**5 years**) --> <!-- * M3 = 2001-2003 (**3 years**) --> <!-- * M4 = 2014-2017 (**4 years**) --> <!-- ] --> <!-- .pull-right[ --> <!-- .center[**Spatial scales**] --> <!-- Ranging from less than **100 Km** `\(^2\)` to **80 000 Km** `\(^2\)` (the entire Czech Republic) --> <!-- ] --> <!-- --- --> <!-- # The Atlas dataset --> <!-- ```{r} --> <!-- for(i in 1:length(shps_names)){ --> <!-- assign( paste0("map", shps_names[i]), --> <!-- get(shps_names[i]) %>% --> <!-- ggplot()+ --> <!-- geom_sf()+ --> <!-- geom_sf(data = shp_country, color = "black", fill = NA)+ --> <!-- coord_sf(xlim = c(12, 19), ylim = c(48.5, 51)) + --> <!-- theme(panel.background = element_blank(), --> <!-- axis.title.x=element_blank(), --> <!-- title = element_blank(), --> <!-- # plot.margin = unit(c(-8,0,-5,2), "cm"), --> <!-- legend.position = "none") --> <!-- ) --> <!-- } --> <!-- ``` --> <!-- ```{r, fig.width=15, fig.height=10} --> <!-- library(cowplot) --> <!-- ggdraw()+ --> <!-- draw_plot(mapm1_kvadraty.shp, x = 0, y = .5, width = .5, height = .5) + --> <!-- draw_plot(mapKvadratyCR_JTSK.shp, x = .5, y = .5, width = .5, height = .5) + --> <!-- draw_plot(mapKvadratyCR_JTSK20.shp, x = 0, y = 0, width = .5, height = .5) + --> <!-- draw_plot(mapKvadratyCR_JTSK40.shp, x = .5, y = 0, width = .5, height = .5) --> <!-- ``` --> <!-- --- --> <!-- # The BBS dataset --> <!-- * Local time series --> <!-- * 350 transects --> <!-- * 20 census points per transect --> <!-- * From 1982 to 2020 --> <!-- * At least 2 censuses per transect and per year --> <!-- * 4 different **spatial scales** --> <!-- * **Temporal scales** ranging from 0.5 year to decades --> <!-- --- --> <!-- # The BBS dataset --> <!-- ```{r} --> <!-- ## Load the database --> <!-- load(file = "../phd/data/czech_bird/JPSP/jpsp_data.Rdata") --> <!-- ## First, replace the error in the CENSUSES_pa db --> <!-- CENSUSES_pa$CensusId[CENSUSES_pa$RecogDist == -4] <- 1 --> <!-- ## Add the rownumber into an id column for the last left_join() --> <!-- Points <- Points %>% rownames_to_column(var = "id") --> <!-- ## Create the vector of transect numbers --> <!-- transID <- unique(Points$Transect) --> <!-- ## Create the tibble that will contain the distance for each transect --> <!-- alldist <- tibble::tibble( --> <!-- id = numeric(), --> <!-- Transect = numeric(), --> <!-- Latitude = numeric(), --> <!-- Longitude = numeric(), --> <!-- sumdist = numeric() --> <!-- ) --> <!-- for (i in 1:length(transID)) { --> <!-- ## Filter the data for the transect --> <!-- tmp <- --> <!-- Points %>% --> <!-- dplyr::filter(Transect == transID[i]) %>% --> <!-- dplyr::select(id, Transect, Latitude, Longitude) --> <!-- ## Create the empty vector that will contain the distance between each point --> <!-- dist <- vector() --> <!-- ## Compute the distance between 2 points --> <!-- for(j in 2:(nrow(tmp) - 1)) { --> <!-- dist[j-1] <- distm(c(tmp$Longitude[j], tmp$Latitude[j]), --> <!-- c(tmp$Longitude[j+1], tmp$Latitude[j+1]), --> <!-- fun = distGeo) --> <!-- } --> <!-- ## Sum the distances to know the length of the transect --> <!-- sumdistm <- sum(dist) --> <!-- ## Update the matrix that contains all the distances --> <!-- alldist <- --> <!-- rbind(alldist, cbind(tmp, sumdistm)) --> <!-- } --> <!-- ## Join the transect distance to the Points database --> <!-- Points <- --> <!-- alldist %>% --> <!-- dplyr::left_join(Points, alldist, by = c("id", "Transect", "Latitude", "Longitude")) %>% --> <!-- column_to_rownames(var = "id") --> <!-- ## Converting the Points dataset into an sf object --> <!-- points_as_shp <- --> <!-- Points %>% --> <!-- filter_at(vars(Latitude, Longitude), any_vars(!is.na(.))) %>% ## the function doesn't accept NA for long and lat --> <!-- st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326) --> <!-- # Computing the convex hull of each transect --> <!-- ## If I want to compute the convex hull of the transect, I need to convert to points into polygons --> <!-- polygons_transect <- --> <!-- points_as_shp %>% --> <!-- filter(Transect != 21) %>% ## add to withdraw the transect 21 composed of only 1 point --> <!-- dplyr::group_by(Transect) %>% --> <!-- dplyr::summarise() %>% --> <!-- st_cast("POLYGON") %>% --> <!-- st_convex_hull() %>% ## transform the inner polygons into outer polygons --> <!-- mutate(transect_area = st_area(.)) ## create the column containing the area --> <!-- ## Convert the m² into km² (*10^(-6)) --> <!-- polygons_transect$transect_area <- set_units(polygons_transect$transect_area, km^2) --> <!-- ## Converting the Points dataset into an sf object --> <!-- points_as_shp <- --> <!-- Points %>% --> <!-- filter_at(vars(Latitude, Longitude), any_vars(!is.na(.))) %>% ## the function doesn't accept NA for long and lat --> <!-- st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326) --> <!-- polygons_transect <- --> <!-- points_as_shp %>% --> <!-- count(Transect) %>% --> <!-- mutate(points_area_200 = (pi*.2^2)*n, --> <!-- points_area_100 = (pi*.1^2)*n) %>% ## compute the area of all points with a radius of 200m --> <!-- as.data.frame() %>% ## because you can't merge 2 sf objects --' --> <!-- select(Transect, points_area_200, points_area_100) %>% --> <!-- merge(polygons_transect, by = "Transect") --> <!-- ## Convert the points area to unit format for sf object --> <!-- polygons_transect$points_area_200 <- set_units(polygons_transect$points_area_200, km^2) --> <!-- polygons_transect$points_area_100 <- set_units(polygons_transect$points_area_100, km^2) --> <!-- ############################################# --> <!-- # Now let's compute the ratio between the hull and the points area --> <!-- polygons_transect <- --> <!-- polygons_transect %>% --> <!-- mutate(polypoint_ratio_200m = ifelse(.$points_area_200 > .$transect_area, --> <!-- 1, .$transect_area/.$points_area_200), --> <!-- polypoint_ratio_100m = ifelse(.$points_area_100 > .$transect_area, --> <!-- 1, .$transect_area / .$points_area_100)) %>% --> <!-- st_as_sf() ## put the data back into sf object --> <!-- ## Set the colors for the points --> <!-- colpal <- colorFactor(topo.colors(20), Points$Point) --> <!-- # colpal2 <- colorFactor(topo.colors(nrow(polygons_transect)), --> <!-- # polygons_transect$polypoint_ratio) --> <!-- # Create the base map --> <!-- m <- --> <!-- leaflet() %>% --> <!-- setView(lat = 50, lng = 15.5, zoom=7.3) %>% --> <!-- addTiles(group="OSM") %>% --> <!-- addPolygons(data = polygons_transect, --> <!-- group = "Transect area") --> <!-- ``` --> <!-- ```{r, out.width="100%"} --> <!-- ## Loop for drawing every transect and points --> <!-- for (i in unique(Points$Transect)) { --> <!-- m <- m %>% --> <!-- addPolylines(data = Points[Points$Transect == i, ], --> <!-- lng = ~Longitude, --> <!-- lat = ~Latitude, --> <!-- label = ~Transect, --> <!-- color = "black", --> <!-- weight = 2) %>% --> <!-- addCircles(data = Points[Points$Transect == i, ], --> <!-- lng = ~Longitude, --> <!-- lat = ~Latitude, --> <!-- label = ~Point, --> <!-- radius = 200, ## In meters --> <!-- color = ~colpal(Point), --> <!-- group = "Points", --> <!-- fillOpacity = .8)%>% --> <!-- addLayersControl( --> <!-- overlayGroups = c("Points", "Transect area"), --> <!-- options = layersControlOptions(collapsed = F)) --> <!-- } --> <!-- m --> <!-- ``` --> <!-- --- --> <!-- class: inverse, center, middle --> <!-- # Data analysis --> <!-- --- --> <!-- # Species richness trend across spatial scales --> <!-- * For each spatial scale, we computed the **species richness trend** (slope of linear regression) --> <!-- * 3 points in time (1987, 2002, 2015) --> <!-- * Harmonization of the two datasets --> <!-- --- --> <!-- # Species richness trend across spatial scales --> <!-- ```{r, out.width="95%"} --> <!-- knitr::include_graphics('images/atlas_maps_boxplot.png') --> <!-- ``` --> <!-- --- --> <!-- # Species richness trend across spatial scales --> <!-- ```{r, out.width="95%"} --> <!-- knitr::include_graphics("images/boxplot.png") --> <!-- ``` --> <!-- --- --> <!-- # Species richness trend across spatial scales --> <!-- .pull-left[ --> <!-- * Increasing species richness trend with spatial scale --> <!-- * Coherent with Chase *et. al* 2019 --> <!-- * Easier extirpation at smaller scales --> <!-- * Lower proportion of extinction with increasing scales (Keil *et. al* 2018) --> <!-- * More habitat heterogeneity at larger scales --> <!-- ] --> <!-- .pull-right[ --> <!-- <br> --> <!-- ```{r, out.width="95%"} --> <!-- knitr::include_graphics("images/boxplot.png") --> <!-- ``` --> <!-- ] --> <!-- .center[ --> <!-- <br> --> <!-- **Question:** is this result observed for a continuum of spatial scales? --> <!-- ] --> <!-- --- --> <!-- class: inverse, center, middle --> <!-- # Modeling --> <!-- --- --> <!-- # Random Forest --> <!-- 1. Understand the drivers of species richness changes --> <!-- 2. Predict the species richness --> <!-- Predictions will allow me to fill the boxplot gaps, spatial and temporal gaps of the datasets --> <!-- <br> --> <!-- **Formula:** --> <!-- ```{r, echo=T, eval=F} --> <!-- randomForest(sr ~ Lat + Long + AREA + Date + polypoint_ratio + time_span) --> <!-- ``` --> <!-- --- --> <!-- # Partial plots --> <!-- .center[ --> <!-- *Species-time relationship (STR) through time* --> <!-- ```{r, out.width="50%"} --> <!-- knitr::include_graphics("images/str_overtime.png") --> <!-- ``` --> <!-- ] --> <!-- --- --> <!-- # Predicitons --> <!-- * For <span style="color: blue;">50 `\(Km²\)`</span> and <span style="color: blue;">10 000 `\(Km²\)`</span> --> <!-- .pull-left[ --> <!-- <br> --> <!-- ```{r, out.width="100%"} --> <!-- knitr::include_graphics("images/50sqkm.png") --> <!-- ``` --> <!-- ] --> <!-- .pull-right[ --> <!-- <br> --> <!-- ```{r, out.width="100%"} --> <!-- knitr::include_graphics("images/10000sqkm.png") --> <!-- ``` --> <!-- ] --> <!-- --- --> <!-- # Predicitons --> <!-- * For <span style="color: blue;">50 `\(Km²\)`</span> and <span style="color: blue;">10 000 `\(Km²\)`</span> --> <!-- .center[ --> <!-- ```{r, out.width="87%"} --> <!-- knitr::include_graphics("images/boxplot_with_predictions.png") --> <!-- ``` --> <!-- ] --> <!-- --- --> <!-- # Next steps --> <!-- <br> --> <!-- * Take into account the sampling effort --> <!-- <br> --> <!-- * Take into account environmental covariates to understand at which scales they interact with biodiversity dynamic --> <!-- <br> --> <!-- * Explore the link with temporal scales --> <!-- <br> --> <!-- * Enlarge the model to Europe --> <!-- <br> --> <!-- * Study other biodiversity metrics and other taxa (lepidopterans, amphibians...) --> <!-- --- --> <!-- class: inverse, center, middle --> <!-- # Thank you for your attention --> <!-- .footnote[ --> <!-- Email: leroy@fzp.czu.cz --> <!-- Twitter: @FrsLry --> <!-- ] --> <!-- --- --> <!-- class: inverse, center, middle --> <!-- ## Supplementary slides --> <!-- --- --> <!-- # Observed vs. predicted --> <!-- .center[ --> <!-- ```{r, out.width="80%"} --> <!-- knitr::include_graphics("images/obs_vs_pred.png") --> <!-- ``` --> <!-- ] --> <!-- --- --> <!-- # SAR and STR --> <!-- .pull-left[ --> <!-- .center[**The SAR**] --> <!-- ```{r, out.width="100%"} --> <!-- knitr::include_graphics("images/sar_rf.jpg") --> <!-- ``` --> <!-- ] --> <!-- .pull-right[ --> <!-- .center[**The STR**] --> <!-- ```{r, out.width="100%"} --> <!-- knitr::include_graphics("images/str_rf.jpg") --> <!-- ``` --> <!-- ] -->